Is then the ability to explicitly (at a high, abstract level) reach down to the initial hypothesis generation and include, raise, or add hypotheses for consideration always a pathology?

I can imagine a system where extremely low probability hypotheses, by virtue of complexity or special evidence required, might need to be formulated or added by high level processes, but you could simply view that as another failure of the generation system, and require that even extremely rare or novel structures of hypotheses must go through channels to avoid this kind of disturbance of natural frequencies, as it were.